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During the Eugenics Wars, the Augments promised freedom from the dictators then in power. Father Robert Welton -- along with 12 cardinals from nation-states in Central and South America -- broke away from the Catholic Church to form the Church of Liberation, and helped the "supermen" overthrow their countries' rulers.

After many governments collapsed during the Eugenics Wars, the Roman Catholic Cardinal Joseph Cerveza was appointed the de facto head of government for the former nation-states of Central America in 1997. The cardinal sentenced Welton to cryogenic freeze and exile in deep space. (Orion Press: "The Return")

With the first contacts with extraterrestrial intelligent species such as the Vulcans and Centaurians in the mid-21st century, Catholicism and its followers underwent a spiritual and cultural upheaval. Such contacts, in many ways, fostered no less a crisis than the events of 1 May 2053, during World War III, where nuclear weapons were detonated above, near, or even in Middle Eastern cities considered sacred by all three major Earth faiths. (The Lost Era novel: The Sundered)

An offshoot of Roman Catholicism emerged in the aftermath of the Third World War, called Neo-Catholicism. Its adherents claimed it was the most doctrinally and socially liberal of the three branches of Roman Catholicism. (Star Trek: Sutherland)

Details of the beliefs and practices of this branch of the Catholic faith were unrevealed.

In 2115, church guidelines and encycllicals from the Fifth Vatican Council (aka "Vatican V") were ratified. One of its resolutions allowed for a non-Terran to be Pope. This caused a major schism within the Catholic Church. (mentioned in Star Trek: Shadowstar Station: "Renée)

During the so-called "Klingon Spring", during which relations between the Federation and Klingon Empire were fairly relaxed, the Roman Catholic Church appointed Kej'ric of the House of Kej'tar Bishop of Qo'noS in 2256. (The Starfleet Museum: Avenger- and Predator-Class Destroyers)

The "Klingon Spring" is contemporaneous with the Four Years War in many other continuities so may never have happened in those continuities -- or happened much earlier.

Gregory the New, an Andorian, was appointed Pope in 2283. ("The Return")